Kyte & Doolittle Hydropathy
Hydropathic regions achieve a positive value. Setting window size to 5-7
is suggested to be a good value for finding putative surface-exposed regions,
whereas a window size of 19-21 yields a plot in which transmembrane domains
stand out sharply, with values of at least 1.6 at their centers.

The Window Position values shown on the x-axis of
the graph reflect the average hydropathy of the entire window, with the
corresponding amino acid as the middle element of that window. For example,
if the window size were 19, the score at window position 10 would be the
average hydropathy of the 19 amino acids from position 1 to position 19
in the input sequence. Notice that the horizontal axis is scaled to include
only those amino acids for which a windowed hydropathy score is computed.

First, each amino acid is given a hydrophobicity score
between -4.5 and 4.5. A score of 4.5 is the most hydrophobic and a score
of -4.5 is the most hydrophilic. Click
here to see each amino acid's score. Then a window size is set. A
window size is the number of amino acids whose hydrophobicity scores will
be averaged and assigned to the middle amino acid in the window. The default
window size is 9 amino acids. The computer program starts with the first
window of amino acids and calculates the average of all the hydrophobicity
scores in that window. Then the computer program moves down one amino
acid and calculates the average of all the hydrophobicity scores in the
second window. This pattern continues to the end of the protein, computing
the average score for each window and assigning it to the middle amino
acid in the window. The averages are then plotted on a graph. The y axis
represents the hydrophobicity scores and the x axis represents the position
in the protein sequence.

Hopp & Woods Antigenic/Hydrophilic
This scale was developed for predicting potential antigenic sites of globular
proteins, which are likely to be rich in charged and polar residues. This
scale is essentially a hydrophilic index, with apolar residues assigned
negative values. The authors suggest that, using a window size of 6,
the region of maximal hydrophilicity is likely to be an antigenic site.